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Hey there, author here! This took a little research: most of the instructions on the internet are for network admins adding local CAs to browsers rather than for users to control who they trust.

We ended up with instructions for configuring the major root stores: OS X, Windows, Firefox and Android. We weren't able to identify a way to choose which iOS 9 inbuilt certificates you trust - Apple Configurator 2 only allows you to add certs.

If HN knows knows how to do this on iOS, let us know!